It Lies Within KOSMOS
by akuma-kisu
Summary: Answers you all have been dying to know about Xenosaga (better than it sounds trust me! i'm aweful at summaries)Chapter two up!
1. The Knowledge you seek

A/N: Um, I guess this is sort of a story where I tried to clarify everything that really confused me in the game. Eh, It's a lot better than it sound so you should R&R!!

Disclaimer: I do no own any part of Xenosaga (though, I wish I did) but only a genius could make a game as brilliant as this, and I sure as hell, am no genius hehe

"That girl," said Shion quietly to herself as she lay on her bed in the Elsa. "Nephilim, who, just who is she?" Shion was laying on her stomach now, her head buried in her pillow. She was still in her Vector uniform, but her jacket was strewn across the chair across from her bed. On the ground next to the chair were her shoes thrown carelessly to the side. She rolled to the side and looked far into the distance.

"She said that in order to endure the future, we needed to face out pasts, but we weren't ready." She let out a long sigh and rolled over once again. For the first time in months, Shion was now able to rest, but she had too many things on her mind to fall asleep.

"Those painful memories…" her voice trailed off. Shion moved her hand and clasped it around her neck where the gnosis had first touched her on the Woglinde.

"Why? Why did this happen? Why did any of this happen?! None of it makes any sense whatsoever!" Shion rolled onto her back and closed her eyes. Her glasses were still set firmly on the bridge of her nose and she wasn't about to take them off either.

"I guess I might as well try to sleep while I can." She whispered as she took a deep breath. Slowly, she found herself drifting off into an uneasy sleep pained with the memories of her journey thus far. Shion groaned a little as she tried to forget. Flashes of her past began flickering in and out of her mind, each of her friends, Jr. Ziggy, MOMO, chaos, followed by KOS-MOS. Then a vision of Kevin and the horrible scene from 2 years earlier, the activation of KOS-MOS, followed by the android's action of destroying thousands of gnosis with her X-Buster. Then the image of Febronia and her awful death of gnosis mercilessly gnawing at her realian flesh along with Nephilim's face appearing slowly as the painful image faded. Shion was witnessing all of it once again in her dreams. The same dreams that haunt her every time she tries to sleep at night. Too painful to forget.

"They are painful," said a quite voice. Shion opened her eyes quickly and jolted out of her bed. She sat up and looked at the wall where her desk was located only to find the silhouette of Nephilim solemnly standing there.

"Wha-what?" stammered Shion who was in shock.

"How did you..." her voice trailed off as she realized she would not get a straight answer.

"You will never forget your past, Shion. That is why I made you face it, to realize that it will always be a part of you, apart of your future as well as a component of KOS-MOS."

"What do you mean, 'A component of KOS-MOS'?" questioned Shion nervously. She was now slowly pulling herself out of bed and making her way over to where Nephilim was standing.

"All your memories are apart of KOS-MOS as well. Even during the painful accident two years ago, KOS-MOS remembers even thought she was destroyed. All of your memories, all of his memories…are apart of her"

"Who's memories? Who is the "he" you are talking about!?" demanded Shion. "None of this is making any sense!" she shouted.

"That's the way he wanted it," Nephilim stated, she paused for a second, looked at Shion and continued. "Two years ago, you lost someone dear to you; it was his wish that KOS-MOS retain all of your memories along with his."

Shion gasped and stared at Nephilim for a long time. "How do you know all of this?" asked Shion skeptically.

"There will be an appropriate time and place when we can discuss that, but now I must enclose to you what I originally came to tell you. I must hurry though, as you know, I can only materialize in your world for short periods of time. It is only when I was able to use KOS-MOS' encephalon, that I was able to stay in that form for such a long period of time."

Shion just paused and continued to stare at Nephilim, waiting for an answer to anything, any one of the million questions she had.

"Most of this is probably very confusing to you. Originally, Shion Uzuki, you were designated as the head of the third division of Vector Inc., the head of the KOS-MOS project, an android designed to combat the threat you know as the gnosis. However, you did not know that the fate of the world was at the mercy of the hands you used to create that android. It was Kevin, however, who knew all of this, yet surprisingly, none of it was disclosed to you. Yet, why then is the KOS-MOS password "Ye Shall be as Gods"?"

Shion was astonished, _how does Nephilim know so much about Kevin, KOS-MOS or me for that matter?? _

"I- I don't know why that password was chosen" admitted Shion. "It was Kevin who originally designated that password to KOS-MOS; I just kept using it when we redesigned her."

"Yes, " said Nephilim, "Do have any idea why that is?"

"No…" said Shion as she looked down at her bare feet.

"It's because KOS-MOS herself can be compared to a God. It is she how will ultimately decide the fate of the world, with her destined battle with the consciousness known as U-DO. It is the password itself which enables KOS-MOS to determine our fate and it is the one thing he wished to have been kept." With that, Nephilim slowly began to fade away, the brightness of her silhouette now fading back into the darkness which Shion had originally hoped for. As Nephilim faded, she left a word of advice for Shion:

"The knowledge that you seek, lies only within KOS-MOS."

Shion stared blankly at the wall where Nephilim had been standing just moments ago.

"It was Kevin's wish?" asked Shion to herself. "Within KOS-MOS?" Shion took a step backward and sat back on her bed with a thump. She was so confused at the entire conversation she had just had with Nephilim.

"Password, Kevin, KOS-MOS, destined battle? None of this is making sense!' Shion screamed again. Shion tried to lay back and go to sleep again, but this time she knew she definitely wasn't going to get much sleep, even though she was extremely tired.

"KOS-MOS" Shion said, just before she managed to fall into a light sleep.

Okay, that's the end of the first chapter so you should all R&R!!


	2. Gnosis Attack

KOS-MOS rox9-Thanks for the review!! And thanks for your comments it's really inspiring!!!

Astragunner2002-Thanks a lot for reviewing my chapter! It's cool that we both have the same interests in how we write!!

Lazychick101-hehe thanks for reviewing all of my stories (at least twice) HA! It means a lot to me when you review, so keep doing it 'kay?

Shion awoke early the next day. She slowly pulled herself out of bed, stretched and yawned.

"What happened last night?" She questioned a loud. She stumbled to the other side of her room to retrieve her jacket and her shoes. She slowly pulled on her jacket. She had a stern look on her face as if she was concentrated hard on something.

"It lies within KOS-MOS?" asked Shion in a rather curios tone of voice. After she had put on her shoes she left her room and walked slowly to the bridge. As the door opened, she saw Allen and chaos talking to each other and Matthews yelling at Tony. Ziggy was standing in the back not saying a word as MOMO and Jr. harassed him about something or other.

"Good morning everyone!" said Shion in a cheerful tone. Everybody stopped what they were doing and turned to Shion. Allen started stuttering in an attempt to greet Shion.

"Uh, um, go-good morning Chief!" stammered Allen as he scratched the back of his head. He blushed a little at his stupidity.

"Good Morning!" said Jr., MOMO, and Ziggy in unison. Matthews just waved and Tony was busy cursing at him under his breath. Shion looked around to see if KOS-MOS was on the bridge as well, but she was no where to be seen. Shion was a little worried because KOS-MOS was usually the first one there.

"Hey, Allen," questioned Shion as she turned to face him, "where is KOS-MOS?"

Allen let out a long sigh under his breath, he was hoping for Shion to talk to him as a person, and not as her subordinate.

"Um, no Chief, I haven't seen KOS-MOS at all this morning. She might still be in the repair room; at least, that's where she was last night…" Allen trailed on. He was getting nervous as Shion kept her steady gaze upon him. Then, she turned away from him and smiled again to the rest of her friends.

"Will you excuse me for a bit?" she questioned, "I'm going to check on KOS-MOS."

Everyone just nodded as Shion left the room. Everyone was silent after her departure, but Jr. broke the silence.

"Nice going!' Jr. scoffed at Allen. "You had a wide open shot too!" MOMO just giggled a bit while chaos just smiled at the depressed Allen. He just sighed and slumped down in the chair where he usually sits.

Shion made her way to the elevator and down to the repair facility where KOS-MOS was hopefully located. Shion's pace sped up just a little as she approached the room. Shion had no idea why she was so nervous to see KOS-MOS, but she was. She opened the door and to her relieve, the blue haired android was standing in the room.

"Oh thank goodness your here KOS-MOS!' gasped Shion. A rush of relief flooded through her. _Why am I so relieved to see KOS-MOS? It's not like anything would have happened to her…_Shion thought to herself.

"Good Morning, Shion." Replied KOS-MOS as she turned to face her creator.

"What are you still doing in here KOS-MOS? I would have thought you would have reported to the bridge by now," stated Shion. KOS-MOS continued looking at Shion.

"There was a problem with sector twelve on the central processing unit in section 38C; I was running repair software that was installed two months and 11 days ago."

"Did it fix the problem?" asked Shion as she took another step toward the android.

"Yes, all systems are functioning within acceptable parameters." Shion frowned a little bit, "Sector twelve? That's odd, we have had problems with that before, maybe I should call Allen so we can check out the problem…" "All of my programs are functioning normally, it would be a misuse of time to run any more software seeing as the problem is no longer apparent, Shion" Shion was sort of thrown off by KOS-MOS' blunt remark and looked at her for a long time, then she turned her head to look at the ground and put her hand to her chin.

"The knowledge you seek, lies within KOS-MOS," said Shion under her breath.

"Hmm, do you have any idea what that means KOS-MOS?" asked Shion as she looked back up at KOS-MOS.

"At the current time, the question you are asking makes no logical sense. The programming that is currently installed is not able to comprehend the illogical thoughts of humans." Shion looked back at the ground and sighed.

"It's alright KOS-MOS; it doesn't make much sense to me either…Maybe I'll understand someday, huh?" Shion smiled as he waited for a reply from KOS-MOS, but she never received one. KOS-MOS just continued to stare at Shion.

"Alright, well it seems that your programs are functioning normally, so everything is fine then!" grinned Shion as she circled around KOS-MOS looking to see if everything was just as it was supposed to be. Just as she was walking around, Shion received a notification from Matthews.

"Hey Miss Vector?" shouted Matthews over the intercom, "you should report to the bridge A.S.A.P. It seems we have some problems here…" after Matthews finished the announcement he turned off the intercom and the room was completely silent.

"Hmm… I wonder what's wrong. Let's go check it out KOS-MOS!" said Shion as she walked towards the exit of the repair facility.

"Yes," replied KOS-MOS as she walked behind Shion. They made it back up to the bridge within a couple minutes and found out what Matthews was talking about.

In the short time that the Elsa had been in hyperspace, they had been completely surrounded by Gnosis. The cargo ship had not been able to detect their presence during that time and without hesitation, came out of hyperspace unsuspectingly, only to find them completely enclosed by gnosis.

Allen was panicking of course while the rest of the crew was thinking of the best course of action.

"Hey Tony," screamed Matthews. "I'm right here! You don't have to yell, ya know?" yelled Tony, just as loud as Matthews had done. Matthews ignored his comment and continued talking.

"Do you think we can put the ship at full throttle and doge 'em all together?" shouted Matthews.

"No, that wouldn't work," commented chaos, "They are closing in too fast, we would never be able to dodge them," Shion looked at the screen that showed the massive number of gnosis enclosing the ship.

"Hmm…" said Shion under her breath. "KOS-MOS?" she asked as she turned her head to look at the android that was standing quietly behind her. Shion's intention was to find out what KOS-MOS had in mind, but she wasn't necessarily prepared for KOS-MOS' response.

"Shion, please allow me to take care of this," said KOS-MOS as she began walking to the back of the room.

"Wait KOS-MOS! You don't need to go!" screamed Shion as the android exited the bridge. Everyone in the room was silent as KOS-MOS left, all except for Shion. She was yelling after KOS-MOS telling her not to go, but KOS-MOS was programmed as an anti gnosis fighting android, and Shion knew it. Still, in the back of her head, there was a tinge of doubt.

"Why are you so worried about KOS-MOS, Shion? She'll be fine! She's handled situations like this before without a problem!" Jr. chimed in. MOMO and Ziggy both nodded their heads in agreement to Jr's statement.

Matthews sat back in his chair and looked over to Shion, who was staring at the door.

"Hopefully she can take care of this; these guys are really startin to become a pain in the ass."

Shion didn't even glance back at Matthew's. She bowed her head and started speaking in a quiet tone of voice.

"Allen, the reason I'm so worried was that while I was checking on KOS-MOS in the repair facility, she mentioned something about a malfunction in sector twelve of the central processing unit," said Shion as she turned to look at him.

"Chief, that shouldn't be much of a problem unless it's…"

"Sector 38C." replied Shion as she finished his sentence for him.

"But, Chief!" yelled Allen, "Why didn't you call me so we could have repaired it!?" Shion's worried expression changed to a small frown.

"I'm not dumb, Allen! I was going to do that, but KOS-MOS said she had already done that." Shion's expression changed back to her depressed look. Allen quieted down from Shion's remark.

"Well, if KOS-MOS said she repaired the problem, then shouldn't it be okay?" Asked Allen trying to make Shion feel a little more comfortable.

"I suppose, but still I can't help wondering if everything is really alright…" Shion's voice trailed off. She looked back at Matthews, "Can you bring up a camera with KOS-MOS location?" asked Shion.

"Sure," replied Matthews in his nonchalant attitude. "She's in the back of the ship, just about to enter the cargo elevator that leads to the top of the ship. Bring up the camera will ya?" Shouted Matthews.

Okay, end of chapter two!!

Chapter preview:

In the next chapter, KOS-MOS fights Gnosis!! But Shion and the group will find out something new about KOS-MOS, so R&R!! Thanks for reading!! I'll try to update soon!!!


	3. NOTICE

NOTICE!!

Hey guys! Thanks for all of your reviews!! They are really inspiring! Anyway, it might take me a while to get chapter three up (finals suck) but I was hoping that some of you could help me out by suggesting things in the game that were unclear to you, I am trying to think of my own theory in a way, so any suggestions you have would be great!! That's a lot!! I should, hopefully, have the next chapter up in about a week!!

Thanks again!


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